feat(runtime): warn when a topology timeout pin is below the default it overrides (#675)

[mrthankyou]

Refs #675.

What's left in #675

The 7200 pin revert and the CI guard on the packaged topologies (#689) landed. What's still open, per the issue's last comment, is the plan-time warning. A node or group timeout_seconds pin outranks the model profile timeout_seconds and run.default_timeout_seconds, even when the pin is the shorter window, and nothing reported it. A project's own topology got no check at all.

Confirmed on unstable (5c1a9775): with default_timeout_seconds = 14400, validate passed the default topology's 7200 pins silently. No source in packages/{topology,config,runtime}/src checks this.

Change

• packages/runtime/src/timeout-shadowing.ts: timeoutShadowingDiagnostics checks each pinned agentic node in the expanded graph. A pinned node is one with a node or group pin. It compares the pin against the default task compilation would apply without it: the node's model profile timeout_seconds, otherwise run.default_timeout_seconds. The profile timeout is read from the config, because expansion folds the run default into each fan-out entry. Each pin below that default produces one TOPOLOGY_TIMEOUT_SHADOWS_DEFAULT warning. The warning names the pin and its path (groups.<id>.defaults.timeout_seconds or nodes.<id>.timeout_seconds), the largest default it overrides, and the nodes it applies to, listing the first three.
• validate adds the warnings to the topology posture, which then reads warn. plan adds them to its diagnostics, and run passes them through.
• The warning changes nothing about resolution. A pin can be a deliberately shorter budget.
• Docs: docs/reference/configuration.md and a CHANGELOG entry.

Not in scope: the model-aware timeout and the finalisation reserve from the original proposal. The issue's comments treat those separately (#680, the runtime's absolute deadline).

Tests

• validate on the shipped default topology gives no warning. With default_timeout_seconds = 14400 it warns for the goals, strategies, specialists and review group pins, and the topology posture is warn.
• plan warns for a group pin (600) and a node pin (300) below the 3600 default, and not for a node pin (7200) above it.
• Ran the two new tests plus the existing validate/plan tests: all pass. Strict eslint and prettier are clean on the changed files. I have not run the full runtime suite locally.

🤖 Generated with Claude Code

Confidence Score: 4/5

The PR should not merge until the duplicate-run precheck handles Smithers stores outside the project-root database path.

Summary

The PR adds warnings when topology timeout pins override longer defaults and adds a pre-planning check for run IDs already recorded by the workflow engine.

• Validation and planning report timeout-shadowing diagnostics without changing timeout resolution.
• The new run-ID check misses engine records for projects whose Smithers store is not at the project-root database path.

_{Reviews (3) · Last reviewed commit: "Merge branch 'unstable' into fix/675-tim..."}